Prototype equestria
by ChaosNightmare12
Summary: A new creature is brought to New York Zero through a transdimensional portal created by Gentek. Both Alex Mercer and Blackwatch wish to use it for their own evil purposes. A lone prototype must save it. Takes place during Prototype 2 and during Season 2 of MLP:FiM.
1. Chapter 1 Saving the mystery beast

James Heller could not believe he was doing this. Helping one of Mercer's Evolved breaking into a Gentek facility..

Heller was looking over the yellow zone, wondering where the next bit of info he'd get was when he got a call. He expected it was from Father Luis Guerra, but was surprised when it was one of Mercer's Evolved. "Who the hell are you and how did you get this number?" He questioned in that oh so endearing tone he was fond of using.

"Please! I don't have much time! Come to this location so we can talk." She asked in a worried tone.

"Why the hell should I?" He demanded.

"Please! Just come! Everything will be explained." She told him.

He sighed. "Fine. I'll be there."

He leapt off the roof.

James landed on a rooftop elsewhere after some leaping and looked around to see where the Evolved was. After a quick look around, he found her sitting in a corner looking at her blade arm. When she noticed Heller's arrival, she turned her weaponized appendage back to normal and got up, saying, "Sell your soul to the devil just to look badass, and all you're left with is regret."

Heller just looked at her like he did most people before finally asking, "Ok, what the hell did you want?"

She sighed (as anyone dealing with Heller worth their salt would) and told him of a Gentek facility holding a Transdimensional portal and a mysterious creature.

"Why the hell should I help you?" Heller demanded.

"Because you want to screw with Mercer and Gentek right?" She asked

"Wait, the hell does Mercer have to do with this?" He asked.

"Well, he wants it because of the possibilities it could open up for the infected and evolved and Gentek wants it because of the possibilities it could open for them." She explained.

"And what about you? What do you get out of this?" He asked.

"One simple thing: an escape." She told him. When he demanded a better answer, much to her surprise, she told him that she had slowly become a Prototype rather than a simple evolved. Afraid that Mercer was starting to notice, she decided to betray him before he did her in.

"Look, I know it sounds cowardly, but I don't want to hurt innocent people anymore." She said crying. Heller realised she was serious.

"Fine. I'll help you. But I'll need to know your name first." He said

"Just call me Sara." She told him. They left for the facility.

BACK AT THE PRESENT

The two Prototypes landed and scouted the building. "Great. Blackwatch guards." Sara grumbled.

"How do you want to take care of this?" Heller asked quietly for once, curious as to what she had in mind.

"First, I lure the two guards out by posing as a scared woman and we consume them. Second, we walk into the facility, changing into a new disguise if we need to. We find the portal and the creature, open the portal, the creature and I escape to its home, you smash the portal controls beyond repair, and steal the data from the computers, making sure that they never find that world or any other. That sound good?"

Heller gave a smirk. "Yep. Let's do it."

On the street, two guards stood at attention, looking around, waiting for their shift to end. One of them asked, "Hey, you ever wonder why we're here?"

Before his buddy could talk, they both saw a woman running out of an ally towards them, panicking audibly. "Please! You gotta help me! My friend is surrounded by those things! She won't last long, please!" She pleaded to the two Gentek mooks.

"Sorry ma'am, we can't leave our p-" The first guard said, before being interrupted by his friend.

"-Don't worry little lady, we'll help your friend." He said in a Texan accent.

"Hey! We're supposed to stay here and guard this place!" The one without a stereotypical accent said while pointing at the ground.

"Don't worry there slick, I'm sure it'll only take couple minutes." He reassured his fellow mook before turning to the young woman. "Now, can you take us to where your friend is miss?" He asked.

"She's this way! Come on!" She said, all the while grabbing his arm and pulling him into a nearby ally.

"Alright, the hell's your friend" The unaccented one asked as Heller dropped down.

"Right behind you." He said in a faux-french accent before consuming the man.

"What in tarnation!" Was all the Texan could say before getting consumed by Sara. "Well that was easy. God, where the hell does Blackwatch find these lemmings? Now let's go find that creature." She said with the dead man's accent.

"Let's just get this over with." Heller groaned.

They walked around for a short while looking for signs of the creature or the portal. "Damn it! Where the hell is that portal!?" Heller complained in his disguise.

"Calm down man! We'll find it!" Sara whispered reassuringly to him just as she opened a door revealing a large purple vortex. "See?" She said as she walked towards the portal, but was stopped by a guard.

"Hey! Do you have clearance to be here?" He asked, suspicious of the two mooks in front of him

"Oh, it's right here." Heller said before bringing out his claws and cutting the guy to ribbons.

"WE GOT EVOLVED! SEAL THE BA-" Another guard screamed before getting cut in half by Sara's blade.

"Great. We got guards." She said sarcastically.

"Well, have you ever played a game called 'highest body count'?" Heller asked.

"Yeah, why?" Sara responded, confused.

"Take a guess." He said with a smirk plastered on his normally grim face.

It took her a second, but by then, the realization hit her like a tank and she slapped herself in the face for not catching on sooner. "You're on." She said with a grin, slashing a guard's head off.

************************************************** ************************************************** ******  
SEVERAL MOMENTS OF GRATUITOUS VIOLENCE LATER

"I win!" Sara exclaimed with a smile.

"Man fuck you! I won!" Heller replied.

"I got fifty-seven. How much did you get?" Sara asked

"So did I. The fuck kind of base has a hundred and forty-seven guards protecting it?" He questioned.

"I don't know...maybe they didn't want to lose the portal and the creature?" She replied, rolling her eyes at how obvious the answer was.

"Speaking of, where the hell is it?" Heller asked. It took a couple seconds to realise that the cage containing the creature was literally right behind him. "Is that-" He cautiously asked in fear of being insane (well, more so, anyways).

"-A purple unicorn?" Sara interrupted. "Yes. Yes it is."

"Huh. You sure they ain't bloodtoxed this place yet?" Heller asked.


	2. Chapter 2 Return

"It's breathing seems to be irregular, Heller." Sara said.

"How do you know that's not just how the thing breaths?" Heller responded, looking around to see if there were more Blackwatch mooks around.

"No. From the reports, it's physiology is the same as a horse or a pony, plus: all of the scratches seems to indicate that it's badly injured. See if you can find something that could help its wounds." She explained as the creature started to open its eyes weakly. Sara checked the pulse of the unicorn and was horrified by what she found: a med pack would not help. Its wounds were too great.

She looked down at the creature she was trying to track down for nearly two weeks, waiting for it to react. The creature, which she now realised was female, talked to her in a language she could not understand, her eyes full of regret, and her tone pleading. Heller said something, but Sara did not pay attention.

"Hey, I found a med pa-what the hell are you doing!?" He screamed as Sara started consuming the creature. He ran towards her, trying to stop her, but was unable to. As Sara started to transform into the unicorn, who she now knew was named Twilight Sparkle, a wave of the equines memories flooded through her.

_"You see, Nightmare Moon, when those Elements are ignited by the... the spark, that resides in the heart of us all, it creates the sixth element: the element of...magic."_

_"I'll tell you what we've learned Discord. We've learned that friendship isn't always easy, but there's no doubt it's worth fighting for. "_

_"Who are you? I mean, you're me, but I'm me too. How can there be two 'me's? It's not scientifically possible. You are not scientifically possible!"_

She was quickly snapped back to reality when Heller knocked her into a wall, holding onto her windpipe ."WHAT THE HELL DID YOU DO!?" He screamed.

"I consumed her because she was not going to survive the next couple minutes, so I gave her a mercy kill. From her memories, she was pretty important in her country." She told him. He loosened his grip, letting her drop down.

"Thanks. Now can you power the portal so I can go 'home' and see everypony." She told him.

"Everypony?" He asked.

"Look, it's how they talk. Just start the portal so I can leave and you can fuck shit up." Sara told him.

He sighed, defeated. "Fine." Heller walked up to the controls. "How the hell do you work this thing!?"

"Green button turns it on, red button turns it off." She deadpanned.

"Well how the hell was I supposed to know that woman!?" He argued.

"There's a sign saying that literally to your left." Sara deadpanned again, pointing to the sign with her hoof before limping to the portal.

"Why the hell are you limping?" He asked.

"I have to make it seem that I was somewhat injured or they would suspect me being an imposter." She told him.

"Well, good luck with that. Now get the fuck out." He retorted before opening the portal.

As Sara walked to the portal, she turned around to wave goodbye to Heller, but she spooted some evolved coming out of nowhere. "We are here for the beast. Give it to us and we'll just pretend you were never here." One of them told Heller.

"Fat chance fugly." Heller insulted as he punched the face of the evolved. One of them looked around. "Wait ,where's Kerrigan? She was supposed to be here with the-" then, his eyes widened when he realised, "THAT BITCH! SHE CONSUMED THE BEAST! KILL HER."

"DAMN IT SARA! RUN!" Heller screamed.

She did as she was told, making her way to the portal and encountering no problems. She jumped in before Heller smashed the controls. Because of this, the portal ride was bumpy to say the least.

When she landed, Sara actually twisted an ankle (do ponies have ankles? Also, oh the irony.) She looked around to see where she was and checked Twilight's memories to see if they could help. Turns out, Sara was inside of the ancient castle of the Royal Pony Sisters. Tired from the trip, she started limping her way out and used her hunter sense to make sure there were no predators. "All I have to do is make it to the edge of the forest and I should be fine." She thought to herself while walking.

When she finally found the exit, Sara collapsed near a cottage because of the exhaustion so didn't see the yellow Pegasus flying towards her.

I got up extra early inside my cottage to make Spike a special breakfast. He's been feeling down ever since Twilight disappeared. I hope she's alright. I went to check on him. Poor kid. Even with all the comforting I gave him, he had been crying himself to sleep for the past two weeks. I can't blame him though. If the closest thing that you had to a mother just vanished out of thin air, you'd have the right to cry. I volunteered to watch the little guy because I knew what it's like to lose your mother. She died when I was just a young filly and nopony should have to go through that alone.

Even Pinky, his girlfriend, tried to cheer him up, but stopped when she realised this was something he had to do himself.

"Hey, Spike! I made you some breakfast! Why don't you come down?" I called out in a caring voice.

"No thanks Fluttershy." He replied in a depressed tone. Poor kid hadn't come down once since he got here.

"Oh...sure...I'll be outside feeding my animals if you need me...ok?" I told him.

I had just finished feeding my bear headed back inside when something caught my eye: a pony collapsing near the everfree forest. Worried that one of the animals of the forest would eat the poor thing, I flew as fast as I could to bring him or her back to my cottage to give him or her proper rest and care.

Who I find shocked me, to say the least. "TWILIGHT!" I shouted, quickly getting her on my back and flying at speeds that would make the sonic rainboom look like my pet snail Gary in comparison. Slowing to a relaxing stroll, I barged right in to my hut shouting, "SPIKE! GET DOWN HERE! I HAVE SOMETHING I NEED YOU TO DO!"

I nearly scared the scales right off the poor guy. "Gah! Fluttershy! Why are you-" He stopped himself once he saw the pony on my back and started to bawl up. "-is...is that...Twilight?"

I just nodded my head. He ran up to me, cried, gave me a hug. "Spike, I need you to send a letter to the Princess. I mean...if you don't mind, that is."

"S-s-sure." He sniveled, wiping away tears and snot before leaving to get a quill and some paper. I put Twilight on the couch so she could sleep comfortably. When Spike got back, I asked him to tell the Princess that I found Twilight by the Everfree Forest and that she was ok. The response said that she was coming to Ponyville within the next couple of hours.


	3. Chapter 3 Reunion of friends

Sara unexpectedly awoke to a sight that she could only describe as odd. It would have freaked her out if it wasn't for Twilight's memories. Oh, and when I say freak out, I don't mean I left the oven on the back home so I'd better get out of wherever I am and turn it off. I mean freak out in the that there's spiders laying eggs in my eyes and they all have explosives attached to them.

But luckily, from the dozens of bird houses and the miniature stairs covering the walls and ceiling, she recognized that this was Fluttershy's house. So, she simply made her new state of consciousness apparent and asked, "Hello?"

Sara's vision was then assaulted by a combination of yellow, pink, purple, and green. "Twilight! Are you alright?" Fluttershy asked.

"Yeah, I think so." She said before being hugged by Spike. Poor thing must have been in a spiral of depression if the bags on his eyes were anything to go by. She embraced him back

"Please, don't go again." Spike mumbled through his tears.

"I won't Spike. I won't." I replied with a somber smile before Rainbow Dash crashed through the door.

Applejack who was behind Rainbow, chastized, "Now, I know you're excited to see Twilight, but you didn't need to go and bust down the door to Futtershy's house there sugarcube."

Rainbow looked around to see said yellow Pegasus shivering behind her couch. "Uh...Sorry Shy."

Pinkie Pie then jumped in, saying, "Oh hi, Sara!"

The abomination in disguise gave her a strange look and asked, "Uh, Pinkie...what did you call me?"

She just giggled and said, "I said: Hi Twi!"

Sara just shook her head, glad that the bouncing mare hadn't grown psychic as well in the time Twilight was missing. "Sorry Pinkie Pie, I must be hearing things."

It was then that Rarity pranced onto the scene like she was the Princess of the universes. "Twilight darling! What happened!? You look like you went to Tartarus and fought Cerberus with a fork!" She exclaimed.

Sara just gave her a deadpan stare.

"Right sorry darling." She apologised, stifling an embarrassed laugh.

Celestia and Luna walked inside, locked in discussion. "Sister, I truly did not expect to be back in Ponyville until tomorrow. What is the reason we came here?" Luna asked, looking confused and depressed about something.

"You will see it Luna." Celestia said smiling, before Luna noticed an adorkable lavender Unicorn mare she had not seen in some time.

"TWILIGHT SPARKLE !YOU HAVE RETURNED!" She shouted in the Royal Canterlot Voice. The force knocked Sara off the couch and onto her twisted hoof. She yelped, wincing at the pain. Luna looked on, horrified at the event and profusely apologised."Twilight! We are sorry! We had no idea you were injured! Please forgive us."

Sara stood up with little effort, keeping weight off her bad hoof and reassured her, smiling,  
"It's okay Princess. I was bound to get off that couch eventually."

She turned to Celestia and began to get nervous just by looking at her. "H-h-hello, Princess Celestia. I'm sorry I can't bow."

The Solar Princess pointed to her hoof. "That is quite alright my faithful student. Now, can you please tell us what happened?"

Sara started to think when all of a sudden, the memories flashed through her mind and not the good ones. She witnessed how Twilight was caught, what they did to her, and how she ended up in the state she was back at Gentek.

Scalpels.

Burning.

Cold.

X-rays.

Digestive patterns.

Bone composition.

Brain activity.

Everything.

Because of this influx of emotions, Sara started crying on the floor, begging to herself to make the images, the memories, stop. Celestia was obviously shocked. "Twilight, you don't need to tell us what happened if the memories are hurting you now, but when you feel more comfortable about it instead. Remember that you can always count on your friends be there for you."

Sara looked up with some tears in her eyes and sniffled out, "T-t-thank you, Princess." She sat there for a few minutes, calming herself down and wiping her eyes dry. She then turned to Fluttershy. "Fluttershy, I think I'm ready to go back home."

Luna gave a funny look and said, "I'll move my stuff out by tomorrow."

Sara gave her a confused look. "Princess, what do you mean by that?"

She looks at her with a half confused, half-embarrassed face. "I thought your friends told you."

Sara slowly shook her head, still trying to wrap it around why an immortal Princess and bringer of the night living in what was now her house for two weeks.

"Oh, well, while you were gone, I served as town librarian. 'Tis nice to have a backup plan in case the whole co-ruler of a country thing goes badly." She joked, smiling.

"Oh...thank you princess." Sara said. That couldn't have been all there was to it, but she didn't question it at the moment. Luna's answer making the room quiet for a few moments supported her hypothesis.

Rainbow then suddenly blurted out, "So, how'd you get back here?"

In stereo, Applejack and Rarity screamed, "RAINBOW!" but Sara intervened, knowing what could happen.

"Girls, it's okay. I just don't want to think about everything that lead up to it much." She said, waving away their concern with a hoof. "To answer your question in a simple way: I came through some sort of portal...and I think I saw a blue box fly past me."

They all looked at me confused, expect for Pinkie, who wore a knowing smile. After that, everypony walked back to the town library. Sara swore she saw a brown earth pony stallion and a grey Pegasus mare enter the blue box from before, but just ignored. I mean, come on! It couldn't have been the TARDIS! That would just be ridiculous!

Because of what she saw though, Sara started to hum the Dr. Who theme.

"Twilight, what are you humming?" Spike asked.

"I don't know." She lied, smiling at the tune. They arrived at her and her number one assistant's swanky abode where everypony said their goodbyes, leaving her, Spike, and Luna left.

"I'll see you later sweety!" Pinkie said before planting a kiss on Spike's cheek and bouncing merrily off. Sara looked at Spike with her best poker face, and considering that she was a shapeshifter that had the skills of about dozen aspiring actors, including James Caan, I'd say it was a pretty darn good one. Spike visibly flinched and Luna giggled like a mad-mare.

"You want to tell me what that was all about?" Sara said, Spike looking at her like he was just caught murdering somepony.

"Well, me and Pinkie started dating a week ago."

She looked at him a few seconds longer and dropped her card shark expression. She replaced it with a motherly smile that only Theresa and Celestia could rival. "I am so happy for you. I'm going to take a shower and head to bed. Wake me when dinner's ready."

He just looked at her, emotions of shock and confusion plastering his face. "So you have no problems with me dating Pinkie?"

Sara just looked at him. With genuine curiosity, she asked, "Why would I be? You're a big drake. You can make some choices for yourself. I'm just wondering what changed your mind from Rarity to Pinkie?"

"Well, Pinkie actually came to see me every day you were gone, as opposed to Rarity, who just visited me once, and after a while, we kinda just, I dunno...hit it off." He explained.

"Okay. Oh, and it's Pinkie and I by the way." Sara smiled before heading to the bathroom. She looked back and noticed that Luna had disappeared, sometime during their conversation no doubt. 'Probably didn't want to make things odd.' She mused.

After her shower, she headed to her room with the plan of rest and taking a book to read just in case. The book she chose was The Origin of Martial Arts by one Master Po. From what the short description of the author told her, he was a panda that lived roughly a thousand years ago and was apparently friends with Princess Luna.

After a short while of reading, she fell asleep having a strange dream. "What the? Why do you look like me? Are you me? No. That's not possible. I'm me. Aren't I?" The strange figure spoke. Before Sara could speak, she was woken up by Spike.

"Twilight! Dinners ready!"

She wiped the sleep from her eyes and trotted downstairs. Sara looked down at the table and only saw a single plate. "I take it that Princess Luna is gone?"

"She left an hour after you fell asleep." He responded.

"And I take it you're going on a date with Pinkie?" She joked.

He scratched the back of his head and blushing, said, "Yeah, actually."

She just smiled at him and pulled out a bag of bits. "Here. My treat."

He shoved the bag away. "I can't accept this."

Sara smiled and told him, "Spike, just take it. It should pay for your expenses tonight. Like I said: my treat." She took a bite out of her food, and after swallowing said, "Besides: you should never make your date pay for your dinner. You either split the bill or you pay for hers."

He was frozen. "Thanks...errr...Twilight." He was shocked not only about the money, but more importantly, that Twilight of all ponies was giving him sound dating advice. He remained frozen as she pushed him out of the door.

"Now go out, and have fun!"

He just turned around and asked, "Are you sure you don't mind?"

Sara just smiled and said, "I'll be fine! Now go and enjoy yourself before I make you!"  
She slammed the door shut. Sara used her hunter sense to see if he was still there before saying to herself, "Finally! The kid's gone! Maybe now I can find out what that dream was all about..."


End file.
